{"id":"https://openalex.org/W2096706242","doi":"https://doi.org/10.1093/bioinformatics/bts700","title":"ECOH: An Enzyme Commission number predictor using mutual information and a support vector machine","display_name":"ECOH: An Enzyme Commission number predictor using mutual information and a support vector machine","publication_year":2012,"publication_date":"2012-12-05","ids":{"openalex":"https://openalex.org/W2096706242","doi":"https://doi.org/10.1093/bioinformatics/bts700","mag":"2096706242","pmid":"https://pubmed.ncbi.nlm.nih.gov/23220570"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/bts700","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bts700","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/29/3/365/48894320/bioinformatics_29_3_365.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"bronze","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/29/3/365/48894320/bioinformatics_29_3_365.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5052391255","display_name":"Yoshihiko Matsuta","orcid":null},"institutions":[{"id":"https://openalex.org/I135768898","display_name":"Ritsumeikan University","ror":"https://ror.org/0197nmd03","country_code":"JP","type":"education","lineage":["https://openalex.org/I135768898","https://openalex.org/I4390039241"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Yoshihiko Matsuta","raw_affiliation_strings":["Department of Bioinformatics, College of Life Sciences, Ritsumeikan University, Shiga, Kusatsu 525-8577, Japan"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Bioinformatics, College of Life Sciences, Ritsumeikan University, Shiga, Kusatsu 525-8577, Japan","institution_ids":["https://openalex.org/I135768898"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5039831856","display_name":"Masahiro Ito","orcid":"https://orcid.org/0000-0001-8364-8440"},"institutions":[{"id":"https://openalex.org/I135768898","display_name":"Ritsumeikan University","ror":"https://ror.org/0197nmd03","country_code":"JP","type":"education","lineage":["https://openalex.org/I135768898","https://openalex.org/I4390039241"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Masahiro Ito","raw_affiliation_strings":["Department of Bioinformatics, College of Life Sciences, Ritsumeikan University, Shiga, Kusatsu 525-8577, Japan"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Bioinformatics, College of Life Sciences, Ritsumeikan University, Shiga, Kusatsu 525-8577, Japan","institution_ids":["https://openalex.org/I135768898"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5037644019","display_name":"Yukako Tohsato","orcid":"https://orcid.org/0000-0001-8378-2383"},"institutions":[{"id":"https://openalex.org/I135768898","display_name":"Ritsumeikan University","ror":"https://ror.org/0197nmd03","country_code":"JP","type":"education","lineage":["https://openalex.org/I135768898","https://openalex.org/I4390039241"]}],"countries":["JP"],"is_corresponding":true,"raw_author_name":"Yukako Tohsato","raw_affiliation_strings":["Department of Bioinformatics, College of Life Sciences, Ritsumeikan University, Shiga, Kusatsu 525-8577, Japan"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Bioinformatics, College of Life Sciences, Ritsumeikan University, Shiga, Kusatsu 525-8577, Japan","institution_ids":["https://openalex.org/I135768898"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5037644019"],"corresponding_institution_ids":["https://openalex.org/I135768898"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":0.6135,"has_fulltext":false,"cited_by_count":39,"citation_normalized_percentile":{"value":0.66194186,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":99},"biblio":{"volume":"29","issue":"3","first_page":"365","last_page":"372"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T12254","display_name":"Machine Learning in Bioinformatics","score":0.3684999942779541,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},"topics":[{"id":"https://openalex.org/T12254","display_name":"Machine Learning in Bioinformatics","score":0.3684999942779541,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.16189999878406525,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10932","display_name":"Microbial Metabolic Engineering and Bioproduction","score":0.13699999451637268,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6536554098129272},{"id":"https://openalex.org/keywords/support-vector-machine","display_name":"Support vector machine","score":0.5607302784919739},{"id":"https://openalex.org/keywords/ranking","display_name":"Ranking (information retrieval)","score":0.5144655704498291},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.4098372459411621},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.4072270393371582},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.382524311542511},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.36065196990966797}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6536554098129272},{"id":"https://openalex.org/C12267149","wikidata":"https://www.wikidata.org/wiki/Q282453","display_name":"Support vector machine","level":2,"score":0.5607302784919739},{"id":"https://openalex.org/C189430467","wikidata":"https://www.wikidata.org/wiki/Q7293293","display_name":"Ranking (information retrieval)","level":2,"score":0.5144655704498291},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.4098372459411621},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.4072270393371582},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.382524311542511},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.36065196990966797}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D004798","descriptor_name":"Enzymes","qualifier_ui":"Q000145","qualifier_name":"classification","is_major_topic":false},{"descriptor_ui":"D004798","descriptor_name":"Enzymes","qualifier_ui":"Q000145","qualifier_name":"classification","is_major_topic":false},{"descriptor_ui":"D004798","descriptor_name":"Enzymes","qualifier_ui":"Q000145","qualifier_name":"classification","is_major_topic":false},{"descriptor_ui":"D009626","descriptor_name":"Terminology as Topic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D009626","descriptor_name":"Terminology as Topic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D009626","descriptor_name":"Terminology as Topic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D060388","descriptor_name":"Support Vector Machine","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D060388","descriptor_name":"Support Vector Machine","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D060388","descriptor_name":"Support Vector Machine","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":2,"locations":[{"id":"doi:10.1093/bioinformatics/bts700","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bts700","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/29/3/365/48894320/bioinformatics_29_3_365.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:23220570","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/23220570","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics (Oxford, England)","raw_type":null}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/bts700","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bts700","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/29/3/365/48894320/bioinformatics_29_3_365.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/17","display_name":"Partnerships for the goals","score":0.41999998688697815}],"awards":[{"id":"https://openalex.org/G1857470898","display_name":"Analysis of robustness of metabolic networks focusing on environmental dependency of gene knockouts","funder_award_id":"23700353","funder_id":"https://openalex.org/F4320334764","funder_display_name":"Japan Society for the Promotion of Science"},{"id":"https://openalex.org/G2381703476","display_name":"Prediction of carbohydrate chain-protein interaction by using carbohydrate chain structure information and its experimental verification","funder_award_id":"22500276","funder_id":"https://openalex.org/F4320334764","funder_display_name":"Japan Society for the Promotion of Science"}],"funders":[{"id":"https://openalex.org/F4320334764","display_name":"Japan Society for the Promotion of Science","ror":"https://ror.org/00hhkn466"}],"has_content":{"pdf":true,"grobid_xml":false},"content_urls":{"pdf":"https://content.openalex.org/works/W2096706242.pdf"},"referenced_works_count":45,"referenced_works":["https://openalex.org/W1532325895","https://openalex.org/W1941659294","https://openalex.org/W1987219907","https://openalex.org/W1996239184","https://openalex.org/W1998767819","https://openalex.org/W2003904638","https://openalex.org/W2009977236","https://openalex.org/W2017661263","https://openalex.org/W2034349524","https://openalex.org/W2034994407","https://openalex.org/W2043799214","https://openalex.org/W2046467381","https://openalex.org/W2049381178","https://openalex.org/W2059444759","https://openalex.org/W2064146062","https://openalex.org/W2070619727","https://openalex.org/W2085176241","https://openalex.org/W2095279025","https://openalex.org/W2098770192","https://openalex.org/W2099619800","https://openalex.org/W2100438221","https://openalex.org/W2103017472","https://openalex.org/W2109943925","https://openalex.org/W2113422307","https://openalex.org/W2118978333","https://openalex.org/W2128653811","https://openalex.org/W2133215312","https://openalex.org/W2145546477","https://openalex.org/W2145661853","https://openalex.org/W2146487442","https://openalex.org/W2148603752","https://openalex.org/W2148797284","https://openalex.org/W2153635508","https://openalex.org/W2171421143","https://openalex.org/W2336141321","https://openalex.org/W2400868534","https://openalex.org/W2945549837","https://openalex.org/W2952213121","https://openalex.org/W2998216295","https://openalex.org/W4213009331","https://openalex.org/W4254721730","https://openalex.org/W4285719527","https://openalex.org/W6675077830","https://openalex.org/W6702813502","https://openalex.org/W7066667914"],"related_works":["https://openalex.org/W2051487156","https://openalex.org/W2073681303","https://openalex.org/W2090763504","https://openalex.org/W148178222","https://openalex.org/W2188500270","https://openalex.org/W2303858293","https://openalex.org/W2544423928","https://openalex.org/W2104657898","https://openalex.org/W1948992892","https://openalex.org/W2052122378"],"abstract_inverted_index":{"MOTIVATION:":[0],"The":[1,194],"enzyme":[2,9,60,217],"nomenclature":[3],"system,":[4],"commonly":[5],"known":[6],"as":[7,200],"the":[8,41,64,75,84,118,129,135,139,144,149,164,167,175,177,182,198,225],"commission":[10],"(EC)":[11],"number,":[12,39],"plays":[13],"a":[14,54,68,97,105,113],"key":[15],"role":[16],"in":[17,29,137,166,208],"classifying":[18],"and":[19,40,81,86,112,132,155,205],"predicting":[20,138,209,216],"enzymatic":[21,70,186],"reactions.":[22],"However,":[23],"numerous":[24],"reactions":[25,42,89,187],"have":[26,35,47,91],"been":[27,92],"described":[28],"various":[30],"pathways":[31],"that":[32,90,128,188],"do":[33],"not":[34,44],"an":[36,48],"official":[37,145],"EC":[38,49,65,102,146,150,171,192,210],"are":[43,152],"expected":[45],"to":[46,83,100],"number":[50,66,147],"assigned":[51],"because":[52],"of":[53,56,67,78,88,134,143,170,184,197],"lack":[55],"articles":[57],"published":[58],"on":[59,74,233],"assays.":[61],"To":[62],"predict":[63,181],"non-classified":[69],"reaction,":[71],"we":[72],"focus":[73],"structural":[76],"similarity":[77],"its":[79,206],"substrate":[80,85],"product":[82,87],"classified.":[93],"RESULTS:":[94],"We":[95,158],"propose":[96],"new":[98],"method":[99,136,178],"assign":[101],"numbers":[103,121,211],"using":[104],"maximum":[106],"common":[107],"substructure":[108],"algorithm,":[109,176],"mutual":[110],"information":[111],"support":[114],"vector":[115],"machine,":[116],"termed":[117],"Enzyme":[119],"COmmission":[120],"Handler":[122],"(ECOH).":[123],"A":[124],"jack-knife":[125],"test":[126],"shows":[127],"sensitivity,":[130],"precision":[131],"accuracy":[133],"first":[140],"three":[141],"digits":[142],"(i.e.":[148],"sub-subclass)":[151],"86.1%,":[153],"87.4%":[154],"99.8%,":[156],"respectively.":[157],"furthermore":[159],"demonstrate":[160],"that,":[161],"by":[162,174],"examining":[163],"ranking":[165],"candidate":[168],"lists":[169],"sub-subclasses":[172],"generated":[173],"can":[179],"successfully":[180],"classification":[183],"85":[185],"fall":[189],"into":[190],"multiple":[191],"sub-subclasses.":[193],"better":[195],"performance":[196],"ECOH":[199,220],"compared":[201],"with":[202],"existing":[203],"methods":[204],"flexibility":[207],"make":[212],"it":[213],"useful":[214],"for":[215],"function.":[218],"AVAILABILITY:":[219],"is":[221],"freely":[222],"available":[223],"via":[224],"Internet":[226],"at":[227],"http://www.bioinfo.sk.ritsumei.ac.jp/apps/ecoh/.":[228],"This":[229],"program":[230],"only":[231],"works":[232],"32-bit":[234],"Windows.":[235]},"counts_by_year":[{"year":2026,"cited_by_count":3},{"year":2025,"cited_by_count":4},{"year":2024,"cited_by_count":2},{"year":2023,"cited_by_count":9},{"year":2022,"cited_by_count":2},{"year":2021,"cited_by_count":2},{"year":2020,"cited_by_count":2},{"year":2019,"cited_by_count":4},{"year":2018,"cited_by_count":2},{"year":2017,"cited_by_count":1},{"year":2016,"cited_by_count":3},{"year":2014,"cited_by_count":4},{"year":2013,"cited_by_count":1}],"updated_date":"2026-07-15T18:14:33.161393","created_date":"2025-10-10T00:00:00"}
